Cook County's government-run pharmacies have been so badly managed the DEA was brought in to help straighten them out.

Pharmacies run by the Cook County Health & Hospitals System dispense a lot of medication – 9,500 outpatient prescriptions a day.

But a months-long investigation by the Better Government Association and CBS2 finds the pharmacies themselves with a share of ailments: Shoddy record keeping and lax security that appear to be facilitating stolen or otherwise missing pharmaceuticals.

Patients and employees relayed stories to the BGA and CBS2 of drugs going missing from Stroger Hospital on Chicago's West Side and other county-run health facilities, and the county's inspector general, who launched his own investigation, was so alarmed by the porous nature of the county's pharmacies he asked the U.S. Drug Enforcement Administration to conduct an in-depth audit.

While those findings have not been formally released, the head of the DEA's Chicago office, Jack Riley, said in an interview that his agency is taking the situation seriously.

He worries that missing medications could end up on the streets, sold illicitly, or otherwise used by drug abusers who end up overdosing.

"These drugs, if not properly accounted for and secured, will kill people . . . and when I see reports like this it doubles our effort to try to make this a better situation for the hospital, but most importantly for . . . the community in which I'm afraid these drugs are gonna end up," Riley said.

The inspector general, the county's in-house watchdog, and documents obtained by the BGA and CBS2, provide some context for the fear:

At least 85 incidents of "missing, lost or stolen pharmaceuticals" were reported from late 2006 to mid-2012. It's unclear whether any of those drugs were ever recovered or any arrests made, and how many other instances went unreported.

Among the missing medications: morphine, vicodin, demerol and oxycodone – potentially addictive narcotic pain killers that are sometimes abused on their own, and sometimes mixed with street drugs for sale and consumption.

The Stroger loading dock where pharmaceuticals arrive is wide open, with virtually anyone able to come and go. And internal controls don't appear to be much better, with record keeping so bad it hasn't always been possible to track what, if any, drugs are missing.

The BGA/CBS2 investigation found county employees are the likely culprits making off with pharmaceuticals.

Marek Piszczatowski, an interpreter employed by the health system to help patients who don't speak English, said he's encountered patients shortchanged on their medications.

"I heard that at least three times" from patients, according to Piszczatowski. "They didn't know what to do. [In one case several months back] everything was in the bag except morphine. It was advanced cancer."

His suspicion: someone at the county pilfered the drugs after the prescription was written, but the patients didn't realize anything was missing until they got home and opened their pill bags. Then it was too late.

A veteran physician who asked to remain anonymous said he's had patients complain over the years about missing drugs, which he suspects were swiped by county employees in at least some of the instances.

Special Agent in Charge (SAC) Jack Riley / www.justice.gov

Two patients interviewed at Stroger in recent days also recounted stories of missing prescriptions.

Stroger's four outpatient pharmacies collectively fill roughly 2,700 prescriptions a day. Four additional outpatient pharmacies at other county health facilities are responsible for another 6,800 daily prescriptions. All told, the county's pharmacy operations are the equivalent of more than a dozen busy Walgreens stores, said county spokeswoman Marisa Kollias.

Many private hospitals, clinics and doctor offices write prescriptions to be filled at off-site pharmacies. But county health facilities fill many prescriptions on-site – at in-house pharmacies – because, in part, many patients can't afford the alternative or aren't able to travel to pick up their medications, county officials said.

There is a silver lining in these grim findings by government investigators and the BGA and CBS2: County health officials seem to be taking things seriously. They've already implemented a better tracking system, and they're cooperating with the DEA to further tighten security and procedures for handling medications, officials said.

Drugs have gone missing for years, sources relayed. While the county health system has many problems – the BGA recently revealed that some county doctors and other medical professionals weren't showing up when they were supposed to, but were still getting paid – the current administration is making changes to professionalize the operation.

Even so, the DEA findings are sure to sting.

"I see no difference in a controlled substance going out the back door of a hospital as I do a Latin King selling heroin with a pistol in his hand on a street corner," Riley said.